fix(gc): sync repodb when gc'ing manifests (#1819)

fix(gc): fix cleaning deduped blobs because they have the modTime of
the original blobs, fixed by updating the modTime when hard linking
the blobs.
fix(gc): failing to parse rootDir at zot startup when using s3 storage
because there are no files under rootDir and we can not create empty dirs
on s3, fixed by creating an empty file under rootDir.

Signed-off-by: Petu Eusebiu <peusebiu@cisco.com>

pkg/api/controller.go

@@ -29,6 +29,7 @@ import (
 	mTypes "zotregistry.io/zot/pkg/meta/types"
 	"zotregistry.io/zot/pkg/scheduler"
 	"zotregistry.io/zot/pkg/storage"
+	"zotregistry.io/zot/pkg/storage/gc"
 )
 
 const (
@@ -338,7 +339,13 @@ func (c *Controller) StartBackgroundTasks(reloadCtx context.Context) {
 
 	// Enable running garbage-collect periodically for DefaultStore
 	if c.Config.Storage.GC {
-		c.StoreController.DefaultStore.RunGCPeriodically(c.Config.Storage.GCInterval, taskScheduler)
+		gc := gc.NewGarbageCollect(c.StoreController.DefaultStore, c.MetaDB, gc.Options{
+			Referrers:      c.Config.Storage.GCReferrers,
+			Delay:          c.Config.Storage.GCDelay,
+			RetentionDelay: c.Config.Storage.UntaggedImageRetentionDelay,
+		}, c.Log)
+
+		gc.CleanImageStorePeriodically(c.Config.Storage.GCInterval, taskScheduler)
 	}
 
 	// Enable running dedupe blobs both ways (dedupe or restore deduped blobs)
@@ -354,7 +361,14 @@ func (c *Controller) StartBackgroundTasks(reloadCtx context.Context) {
 		for route, storageConfig := range c.Config.Storage.SubPaths {
 			// Enable running garbage-collect periodically for subImageStore
 			if storageConfig.GC {
-				c.StoreController.SubStore[route].RunGCPeriodically(storageConfig.GCInterval, taskScheduler)
+				gc := gc.NewGarbageCollect(c.StoreController.SubStore[route], c.MetaDB,
+					gc.Options{
+						Referrers:      storageConfig.GCReferrers,
+						Delay:          storageConfig.GCDelay,
+						RetentionDelay: storageConfig.UntaggedImageRetentionDelay,
+					}, c.Log)
+
+				gc.CleanImageStorePeriodically(storageConfig.GCInterval, taskScheduler)
 			}
 
 			// Enable extensions if extension config is provided for subImageStore